Dataset Information

Quantitative Proteome Profiling of Maize Root zones Provides Insight into the Proteins Associated with Enhance Water Uptake in Maize

ABSTRACT: In order to get a better understanding of protein functions related to water uptake in maize, we investigated the proteome dynamics of cv. Anyu308 root system at three key zones divided into Upper root (0cm-20cm), Middle root (20cm-40cm), and Lower root (40cm-60cm) by label-free quantitative shotgun proteomic approach (LFQ). A total of 489 differentially abundant proteins (DAPs) were identified in cv. Anyu308 root in a pairwise comparison of MR, LR, and UR, including shared and unique DAPs in the three root zones, respectively. Cluster analysis revealed MR and LR had similar protein expression patterns different from UR. Comparisons of protein profile indicate that more protein abundance changes occurred in MR, whereas more DAPs were downregulated in the LR and UR. Expression patterns, functional category, and pathway enrichment analyses highlight chromatin structure and dynamics, ribosomal structures, polysaccharide metabolism, energy metabolism, transport, inorganic ion transport, intracellular trafficking, and vesicular transport posttranslational modification as primary biological processes related to maize root water uptake. Furthermore, the accumulation of histones, ribosomal proteins, and aquaporins, including mitochondrion electron transport proteins and the TCA cycle, underpinned MR's high-water uptake. The results also indicated that the proteins involved in vascular transport, protein folding, and proteolysis supported the radial transport of solute across cell membranes in MR. Parallel reaction monitoring (PRM) analysis confirmed the expression profile of the proteins obtained by LQF-based proteomics. The current results provided an insight into the mechanisms of enhancing root water uptake in maize.

ORGANISM(S): Zea Mays

SUBMITTER: Chuankui Chen

PROVIDER: PXD026269 | iProX | Wed May 26 00:00:00 BST 2021

REPOSITORIES: iProX

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Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake.

Song Junqiao J Lu Daowen D Niu Yongfeng Y Sun Haichao H Zhang Pan P Dong Wenheng W Li Yongjiang Y Zhang Yingying Y Lu Lianyong L Men Qi Q Zhang Xiaohui X Ren Pengxun P Chen Chuankui C

BMC genomics 20220306 1

<h4>Background</h4>Maize is one of the most important food crops worldwide. Roots play important role in maize productivity through water and nutrient uptake from the soil. Improving maize root traits for efficient water uptake will help to optimize irrigation and contribute to sustainable maize production. Therefore, we investigated the protein profiles of maize cv. Anyu308 root system divided into Upper root zone (UR), Middle root (MR), and Lower root (LR), by label free quantitative shotgun p ...[more]

PMID: 35247985

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Project description:Previous work showed that the maize primary root adapts to low water potential (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low water potential. To identify mechanisms that determine these responses to low water potential, transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation. Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit. The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone. Keywords: water stress response, root growth Three pair-wise comparisons were made of transcripts from water-stressed and well-watered tissues in the different root tip regions. In the first comparison (C1), transcripts from region 1 of water-stressed seedlings were compared with those from region 1 of well-watered seedlings. The second comparison (C2) was made between transcripts from region 2 of the two treatments. We expected a larger number of genes to be differentially expressed in region 2 because its elongation rate decreased greatly under water-stressed compared with well-watered conditions. To prioritize the differentially expressed genes revealed in this comparison, a distinction was made between those genes that are associated with growth inhibition in region 2 specifically as a response to water stress, and those genes that are involved in root cell maturation whether under stress or control conditions. A hypothetical example of the former might be genes involved in auxin response since water stress can increase maize root auxin content [8] and application of exogenous auxin can shorten the root growth zone [9]. An example of the latter might involve genes for secondary wall synthesis, e.g., [10]. To experimentally make this distinction a third pair-wise comparison (C2/3) was included to compare expression of genes between water-stressed region 2 and well-watered region 3 as these are both regions of cell maturation. Genes differentially expressed in both C2 and C2/3 are more likely to cause growth inhibition at low water potential and are not likely to be part of the maturation program itself, whereas genes differentially expressed only in C2 are more likely related to maturation. Four biological replicates were included each with dye-swap. The maize oligonucleotide array comes in two slides, A and B. Thus for each of the three comparisons made there were 16 slides (4 biological reps, 2 for dye-swap, 2 parts to an array).

Dataset Information

Quantitative Proteome Profiling of Maize Root zones Provides Insight into the Proteins Associated with Enhance Water Uptake in Maize

Publications

Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake.

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